[R] interactions feature in RF?

Hi all, Is there a possibility of getting the interactions feature values for the variables of a dataset by applying the Random Forest algorithm? Thanks, Chrysanthi [[alternative HTML version deleted]] __ R-help@r-project.org mailing list

Re: [R] how to visualize gini coefficient in each node in RF?

that? thanks a lot, chrysanthi 2009/9/29 Liaw, Andy andy_l...@merck.com No. The forest object is too large as is. I didn't think it's worth the extra memory to store them. They were never kept even in the Fortran/C code. Andy From: Chrysanthi A. Sent: Monday, September 28, 2009 5:20

[R] how to visualize gini coefficient in each node in RF?

? Thanks a lot, Chrysanthi [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented

[R] Gini importance measure in RF package

? Thanks a lot, Chrysanthi [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented

[R] Gini importance measure in RF package

? Thanks a lot, Chrysanthi [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented

Re: [R] Problem with Random Forest predict

? Thanks a lot, Chrysanthi [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented

Re: [R] heatmap.2: question regarding the raw z-score

differentially expressed in the two subtypes of the disease that I examine. Many thanks, Chrysanthi. 2009/7/8 James W. MacDonald jmac...@med.umich.edu Hi Chrysanthi, Chrysanthi A. wrote: Hi, I am analysing gene expression data using the heatmap.2 function in R and I was wondering what

[R] heatmap.2: question regarding the raw z-score

value - mean of the group) / standard deviation. But, mean of which group? Mean of the gene vector? And actual value of that gene on a sample? I would be grateful if you could give me some more details about it or even if there is a book/manual that I could address to.. Thanks a lot, Chrysanthi

Re: [R] help with random forest package

). The best way to do that is using caret package, or has RF any option for that? Many thanks, Chrysanthi. 2009/4/28 Liaw, Andy andy_l...@merck.com Let's try an example: R iris.1tree - randomForest(Species ~ ., data=iris, ntree=1) R getTree(iris.1tree, 1) left daughter right daughter

Re: [R] help with random forest package

was wondering why randomizations along with combining the predictions from the trees significantly improve the overall predictive accuracy? Thanks a lot, Chrysanthi 2009/4/13 Liaw, Andy andy_l...@merck.com I really don't understand what you don't understand. Do you know how a tree forms

Re: [R] help with random forest package

But how does it estimate that voting output? How does it get the 85.7% for all the trees? Regarding the prediction accuracy. If I have OOB error = 2.34, then the prediction accuracy will be equal to 76.6%, right? Many thanks, Chrysanthi. 2009/4/13 Liaw, Andy andy_l...@merck.com RF forms

[R] Running random forest using different training and testing schemes

that? Is there a function? Thanks a lot, Chrysanthi. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting

Re: [R] Running random forest using different training and testing schemes

Thanks a lot for your help.. But, using this function, how can identify the size of the training set? and how will I identify my data? There is not any example and I am a bit confused. Many thanks, Chrysanthi 2009/4/12 Max Kuhn mxk...@gmail.com There is also the train function in the caret

Re: [R] Re : Running random forest using different training and testing schemes

Hi Pierre, Thanks a lot for your help.. So, using that script, I just separate my data in two parts, right? For using as training set the 70 % of the data and the rest as test, should I multiply the n with the 0.70 (for this case)? Many thanks, Chrysanthi 2009/4/12 Pierre Moffard pier.m

Re: [R] help with random forest package

have OOB estimate of error rate:2.34%, we can say that the prediction accuracy is approx. 97.7%? How can we estimate the prediction accuracy? Thanks a lot, Chrysanthi. 2009/4/8 Liaw, Andy andy_l...@merck.com I'm not quite sure what you're asking. RF predicts by classifying the new

[R] help with random forest package

during the construction of each tree? I mean, that I would like to know the mM variables that are selected at each node out of the M input attributes.. Are they selected randomly? Is there a possibility to select the same variable in subsequent nodes? Thanks a lot, Chrysanthi

Re: [R] help with random forest package

Many thanks for the reply. So, extracting the votes, how can we clarify the classification result? If I want to predict in which class will be included an unknown sample, what is the rule that will give me that? Thanks a lot, Chrysanthi. 2009/4/8 Liaw, Andy andy_l...@merck.com The source